Unusual "ENOENT" error when trying to run fMRIPrep

Software Support
1

Summary of what happened:

Hi! I’m new to using fMRIprep and am experiencing an error when trying to run an example tutorial. The tutorial I’m following is this one: Using fmriprep for fMRI data preprocessing | by Gelana Tostaeva | Medium. I’ve cloned and copied the entire dataset for the tutorial and I have got the following error when trying to run fMRIPrep. Can anyone figure out what this is all about as I’m a little stuck! Thanks in advance!
Best,
Steve

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep-docker \
/Users/steve/ml_projects/fMRIprep/data/ds000052/ \
/Users/steve/ml_projects/fMRIprep/data/ds000052/output \
participant \
--participant-label 01 \
--fs-license-file /Users/steve/ml_projects/fMRIprep/license.txt

This translates to a call of:

docker run \
--rm \
-e DOCKER_VERSION_8395080871=26.1.4 \
-it \
-v /Users/steve/ml_projects/fMRIprep/license.txt:/opt/freesurfer/license.txt:ro \
-v /Users/steve/ml_projects/fMRIprep/data/ds000052:/data:ro \
-v /Users/steve/ml_projects/fMRIprep/data/ds000052/output:/out \
nipreps/fmriprep:24.0.0 \
/data /out participant \
--participant-label 01

Version:

24.0.0

Environment (Docker, Singularity / Apptainer, custom installation):

Docker
macOs Monterey
Macbook pro (16-inch 2019)
Processor 2,6 Ghz 6-Core intel Core I7
Memory 16 GB 2667 MHz DDR4
Startup Disk Macintosh HD

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

Warning: <8GB of RAM is available within your Docker environment.
Some parts of fMRIPrep may fail to complete.
Continue anyway? [y/N]y
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=26.1.4 -it -v /Users/steve/ml_projects/fMRIprep/license.txt:/opt/freesurfer/license.txt:ro -v /Users/steve/ml_projects/fMRIprep/data/ds000052:/data:ro -v /Users/steve/ml_projects/fMRIprep/data/ds000052/output:/out nipreps/fmriprep:24.0.0 /data /out participant --participant-label 01
bids-validator@1.14.6
(node:9) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
Unhandled rejection (
  reason: Error: ENOENT: no such file or directory, scandir '/data/.git/annex/objects/W5'
).

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/bin/fmriprep", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/cli/run.py", line 40, in main
    parse_args()
  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/cli/parser.py", line 903, in parse_args
    validate_input_dir(
  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/utils/bids.py", line 245, in validate_input_dir
    subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name])  # noqa: S607
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.11/subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bids-validator', '/data', '-c', '/tmp/tmp_356zewm.json']' returned non-zero exit status 3.
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues

Screenshots / relevant information:

2

Hi @Steve_Sizzou,

For future posts like this, please organize and categorize your post to the Software Support category template. You can see I did it for you this time.

In regards to your error, I am guessing you used Datalad or something to clone the repository, and the symlinks involved in that are confusing Docker. You might have more success using the docker run method and being more hands on with binding drives to the container, as symlinks often require more careful consideration. In particular, not renaming the drive when mounting, or mounting a drive as itself, may help.

Best,
Steven